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                            <h2 style="color: #7030A0;
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                                font-weight: bold">Cucume</h2>
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                        <p style="font-size: 20px;">
                            Address for the potential correlations between RNA methylation, RNA mobility and QTL from
                            <span style="color: #C00000">Epitranscripome Sequencing Data</span>
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                <h3>Welcome to Cucume!</h3>

                <p style="text-indent: 2em;"><b>The Cucurbit RNA methylation Database (Cucume)</b> is dedicated to the collection and standardization of data on Cucurbitaceae RNA methylation sites.Due to the extensive influence of RNA methylation on plant developmental physiology and stress response, we added the cucumber Quantitative trait locus (QTL) and the phloem-mediated long-distance transport RNA datasets in cucumber and pumpkin.
                </p>

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                        <span class="area_title" >Introduction</span>
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                                In plants, as most common RNA methylations, N6-methyladenosine (m<sup>6</sup>A) and
                                5-methylcytosine (m<sup>5</sup>C) play important dynamic roles in many biological processes,
                                including embryonic development, stem cell fate determination, trichome branching,
                                leaf morphogenesis, floral transformation, stress response, fruit maturation and root development.
                                m<sup>6</sup>A modification plays a vital role in almost every aspect of mRNA metabolism,
                                including alternative splicing, 3’-end processing, nucleocytoplasmic shuttling, translation, and mRNA decay.
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                        <span class="area_title" >RNA methylation sites</span>
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                                The Cucurbit RNA methylation Database (Cucume) is dedicated to the collection and
                                standardization of data on Cucurbitaceae RNA methylation sites (Fig.1).

                            </p>
                            <p style="text-indent: 2em;
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                                Fig.1: In this part, methylation sites of total RNA were analyzed and combined in both
                                adult plants of cucumber (Cucumis sativus L. ‘Xintai Mici’) (A) and pumpkin (Cucurbita
                                moschata ‘Qianglishi’) (B) respectively and vascular exudation of them (C) by using
                                Methylated RNA Immunoprecipitation sequencing (MeRIP-seq) (D). Preliminary analysis
                                included Metagene profiles of methylation peaks along 5’UTR, CDS and 3’UTR (E).


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                        <span class="area_title" >Quantitative Trait Locus</span>
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                            <p style="text-indent: 2em;
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                                Due to the extensive influence of RNA methylation on plant developmental physiology and
                                stress response, we added the cucumber Quantitative trait locus (QTL) and the phloem-mediated
                                long-distance transport RNA datasets in cucumber and pumpkin.
                            </p>
                            <p style="text-indent: 2em;
                                font-size: 16px;">
                                Fig.2: The datasets of QTL regions were obtained from publicated literature, which contains
                                287 cucumber QTL for 31 quantitative traits. These traits are including QTL for whole plant
                                vegetative growth and development, reproductive development, fruit–related traits, seed-related
                                traits and disease resistances and abiotic stress tolerances. QTL mapping studies for these
                                traits were conducted using multiple recombinant inbred lines populations such as the following
                                crosses: 9110Gt × 9930, Gy14 × B10 and PI 183967 × 931. Through database integration of QTL interval
                                information and RNA methylation sequencing results, the intensity of methylation distribution
                                can be analyzed, and the potential association with agronomic traits can be explored.

                            </p>
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                            <b>Fig.2</b>
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                        <span class="area_title" >Mobile RNA datasets</span>
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                            <p style="text-indent: 2em;
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                                The datasets of mobile RNA molecules in cucumber and pumpkin were obtained from publication
                                by using grafting with RNA-sequencing strategy (Fig.3)(Liu et al.,2020).

                            </p>
                            <p style="text-indent: 2em;
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                                Fig.3:Hypocotyl grafting of <i>Cucumis sativus</i> and <i>Cucurbitea moschata</i> seedlings.(A)
                                    <i>Cucumis sativus</i> (scion)/<i>Cucurbitea moschata</i> (rootstock) (Csa/Cmo) and
                                    reverse grafting (Cmo/Csa) heterograft combinations and homografts (Csa/Csa, Cmo/Cmo).
                                    (B) Graft-union magnification of Csa/Cmo shown in (A); arrowheads indicate graft union
                                    (GU). (C). Scion-to-rootstock long-distance movement of heterologous mRNAs through the
                                    phloem was identified in hypocotyl-grafted cucurbits. If Csa transcripts (red) moved to
                                    Cmo stock across the grafting union, they could be distinguished from Cmo transcripts
                                    (black) based on genomic single nucleotide polymorphism (SNP) differences. The first
                                    true leaf and whole root were sampled for further analyses. Dotted arrow indicates
                                    rootstock-to-scion mobile Cmo transcripts (black) moving to Csa through cell-to-cell
                                    spread or a cycle pathway of scion-to-rootstock-to-scion.


                            </p>
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                            <b>Fig.3</b>
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                <p style="font-size: 16px;
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                    The developed database can visualize methylation peaks based on JBrowse. The resulting network mappings
                    provide a basis for detecting the patterns of the potential role of RNA methylation (m<sup>5</sup>C,
                    m<sup>6</sup>A) in RNA signaling and agricultural traits, and further understanding their performance
                    in plant signaling transduction and developmental biology.
                </p>
                <p style="font-size: 16px;
                    text-indent: 2em;">
                    The Cucurbit RNA methylation Database will continue to be maintained to provide help for the study of
                    RNA functions and genetic feature related to the methylation of Cucurbitaceae.</p>
            </div>

            <div class="index-right" style="text-align: center">
                <img src="/assets/images/fig1.jpg" style="width: 100%;margin-top: 45px"/>
                <b>Fig.1</b>

                <div style="text-align: center" id="img-fig2" class="img-fig">
                    <img src="/assets/images/fig2.jpg" style="width: 100%"/>
                    <b>Fig.2</b>
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                <div style="text-align: center" id="img-fig3" class="img-fig">
                    <img src="/assets/images/fig3.jpg" style="width: 100%;"/>
                    <b>Fig.3</b>
                </div>
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        </div>

        <div class="index-box"  style="padding-top: 5px">
            <div class="index-left" style="width: 100%">
                <h4>References</h4>

                <p>1.Thieme, C. J., Rojas-Triana, M., Stecyk, E., Schudoma, C., Zhang, W., Yang, L., et al. (2015). Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat. Plants 1:15025. doi: 10.1038/nplants.2015.25
                </p>
                <p>2. Yang, L., Perrera, V., Saplaoura, E., Apelt, F., Bahin, M., Kramdi, A., et al. (2019). M<sup>5</sup>C methylation guides systemic transport of messenger RNA over graft junctions in plants. Curr. Biol. 29:2465. doi: 10.1016/j.cub.2019.06. 042
                </p>
                <p>3.Zhang, W., Thieme, C. J., Kollwig, G., Apelt, F., Yang, L., Winter, N., et al. (2016). tRNA-related sequences trigger systemic mRNA transport in plants. Plant Cell 28, 1237–1249. doi: 10.1105/tpc.15.01056
                </p>
                <p>4.Liu, W., Xiang, C., Li, X., Wang, T., Lu, X., Liu, Z., et al. (2020). Identification of long-distance transmissible mRNA between scion and rootstock in cucurbit seedling heterografts. Int. J. Mol. Sci. 21:5253.
                </p>
                <p>5.Wang, T., Li, X., Zhang, X., Wang, Q., Liu, W., Lu, X., Gao, S., Liu, Z. Liu, M.,Gao, L. and Zhang, W. (2021). RNA motifs and modification involve in RNA long-distance transport in plants. Frontiers in cell and developmental biology. 9: 651278.
                </p>
                <p>6. Wang, Y., Bo, K., Gu, X., Pan, J., Li, Y., Chen, J., Wen, C., Ren, Z., Ren, H., Chen, X., Grumet, R., Weng, Y. (2020) Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Hortic Res. 1;7:3.
                </p>
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